<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
	"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta http-equiv="Content-Style-Type" content="text/css">
<link rel="stylesheet" type="text/css" href="gmaj.css">
</head>
<body>
<p class=vvlarge>
<h2>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</h2>
<p class=vvlarge>
Gmaj is a tool designed for viewing and manipulating Generalized
Multiple Alignments (GMAs) produced by sequence-symmetric alignment
programs such as <a href="http://www.bx.psu.edu/miller_lab/">TBA</a>
(though it can also be used with MAF format alignments from other
sources).  It can display interactive graphical and text
representations of the alignments, diagrams showing the locations
of exons and repeats, and other annotations -- all with the user's
choice of reference sequence.
<p>
The program is written in Java in order to provide a graphical
user interface that is portable across a variety of computer
platforms; indeed its name stands for "Generalized Multiple
Alignments with Java".  It requires <b>Java 1.3 or higher</b>,
and for best compatibility
<a href="http://java.com/en/download/manual.jsp">Sun's JRE</a>
(or JDK) is recommended.
<p>
Gmaj can be run in two different modes: as a stand-alone
application (for viewing local data files yourself) or as an
applet over the world-wide web (to display your data on a server
for viewing by others).  These modes are mostly similar, but
have a few minor differences due to the underlying capabilities
of applets vs. applications in Java.
<p>
<blockquote class=notop>
<a href="http://globin.bx.psu.edu/java/gmaj/demo.html"
>Applet demo</a>
</blockquote>
<p class=large>
The current Gmaj distribution package is available for download
as a compressed zip archive,
<code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip"
>gmaj.zip</a></code>.
<p>
The following additional documentation files are included:
<ul>
<li>	<a href="gmaj_news.html">What's New in Gmaj</a><br>
	A summary of the changes in each released version of Gmaj.
	(Note important <b>bug fix</b> on 2005-Sep-13.)
<p>
<li>	<a href="gmaj_bugs.html">Known Bugs in Gmaj</a><br>
	A discussion of the known bugs and anomalies we have
	observed, but not yet resolved.  Some of these may depend
	on your computer platform and/or version of Java.
<p>
<li>	<a href="gmaj_install.html">Installing Gmaj</a><br>
	Describes how to unpack and set up Gmaj, for both
	stand-alone and applet use.
<p>
<li>	<a href="gmaj_help.html">Starting and Running Gmaj</a><br>
	Describes how to start Gmaj and use the GUI, in both
	stand-alone and applet modes.  This is the file that Gmaj's
	"Help - Manual" menu item points to.
<p>
<li>	<a href="gmaj_input.html">Input Files for Gmaj</a><br>
	Detailed descriptions of the input files used by Gmaj, and
	their formats.
<p>
<li>	<code><a href="sample.gmaj">sample.gmaj</a></code><br>
	A sample template for the parameters file that tells Gmaj
	which data files to load, among other things.  Includes
	explanatory comments at the bottom.  This file is optional
	if you don't want to display any annotations or use the
	other features it provides.
</ul>
<p>

<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2008</i>
</body>
</html>
